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Test multiple bases and intervals

This commit is contained in:
Joel Thibault 2012-11-19 14:44:00 -05:00
parent c08b782743
commit e8defcb20d
1 changed files with 45 additions and 20 deletions
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65
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -83,49 +83,74 @@ public class TraverseActiveRegionsTest extends BaseTest {
}
@Test
public void testAllIntervalsSeen() throws Exception {
public void testAllBasesSeenSuite() {
List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
List<GenomeLoc> activeIntervals = new ArrayList<GenomeLoc>();
GenomeLoc interval = genomeLocParser.createGenomeLoc("1", 1, 1);
intervals.add(interval);
testAllBasesSeen(intervals);
LocusShardDataProvider dataProvider = createDataProvider(intervals);
interval = genomeLocParser.createGenomeLoc("1", 10, 20);
intervals.add(interval);
testAllBasesSeen(intervals);
}
t.traverse(walker, dataProvider, 0);
activeIntervals.addAll(walker.isActiveCalls);
public void testAllBasesSeen(List<GenomeLoc> intervals) {
List<GenomeLoc> activeIntervals = new ArrayList<GenomeLoc>();
for (LocusShardDataProvider dataProvider : createDataProviders(intervals)) {
t.traverse(walker, dataProvider, 0);
activeIntervals.addAll(walker.isActiveCalls);
}
boolean allGenomeLocsSeen = true;
for (GenomeLoc loc : intervals) {
boolean thisGenomeLocSeen = false;
boolean allBasesSeen = true;
for (GenomeLoc base : toBases(intervals)) {
boolean thisBaseSeen = false;
for (GenomeLoc activeLoc : activeIntervals) {
if (loc.equals(activeLoc)) {
thisGenomeLocSeen = true;
if (base.equals(activeLoc)) {
thisBaseSeen = true;
break;
}
}
if (!thisGenomeLocSeen) {
allGenomeLocsSeen = false;
if (!thisBaseSeen) {
allBasesSeen = false;
break;
}
}
Assert.assertTrue(allGenomeLocsSeen, "Some intervals missing from activity profile");
Assert.assertTrue(allBasesSeen, "Some intervals missing from activity profile");
}
private LocusShardDataProvider createDataProvider(List<GenomeLoc> intervals) {
private List<GenomeLoc> toBases(List<GenomeLoc> intervals) {
List<GenomeLoc> bases = new ArrayList<GenomeLoc>();
for (GenomeLoc interval : intervals) {
if (interval.size() == 1)
bases.add(interval);
else {
for (int location = interval.getStart(); location <= interval.getStop(); location++) {
bases.add(genomeLocParser.createGenomeLoc(interval.getContig(), location, location));
}
}
}
return bases;
}
private List<LocusShardDataProvider> createDataProviders(List<GenomeLoc> intervals) {
walker = new DummyActiveRegionWalker();
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>());
Shard shard = new MockLocusShard(genomeLocParser, intervals);
WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
//engine.setReferenceDataSource(reference);
engine.setGenomeLocParser(genomeLocParser);
t.initialize(engine);
return new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>());
Shard shard = new MockLocusShard(genomeLocParser, intervals);
List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
for (WindowMaker.WindowMakerIterator window : windowMaker) {
providers.add(new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
}
return providers;
}
}